(unknown charset) [AMBER] Queastions Regarding Tutorial A11 NCSU Method

From: (unknown charset) Γιώργος Λαμπρινίδης <lamprinidis.pharm.uoa.gr>
Date: Mon, 8 Oct 2012 22:48:17 +0300

Dear users,

I was trying to run a simulation according to Tutorial A11 (Pyranose ring
puckering)
When I finish the "finer" run using Implicit solvent i get a restart file,
containing the final velocities. In order to create the explicit solvent
job i transform prmtop and inpcrd files to pdb and I use tleap to create
the solvated files and i export them. With this procedure I loose all
velocities, so when i try to run the "flooding" procedure using the mdin
file from the tutorial i get an error "no velocities found", because of
the "irest =1, ntx =5" command.
How can overcome this error? Propably i am missing something.
In the tutorial how from the restart file of implicit solvent someone goes
to "flooding" using explicit water?

Thank for your time,
George Lamprinidis

-- 
Dr Giorgos Lamprinidis
Researcher & Laboratory Assistant Staff
Faculty of Pharmacy
University of Athens - Greece
tel: +30 2107274304
     +30 2107274824
fax: +30 2107274747
e-mail: lamprinidis.pharm.uoa.gr
        geolampr.gmail.com
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Received on Mon Oct 08 2012 - 13:00:03 PDT
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